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Governor Deval Patrick’s dramatic shake-up of the Parole Board and proposed crackdown on habitual, violent criminals will probably aggravate overcrowding in a prison system that is nearly 40 percent over capacity, according to criminologists and advocates for inmates.

Like many other states, Massachusetts has struggled to find room for its inmates, with the prison population more than tripling over the past two decades to well over 11,000. At a time when other financially strapped states are under federal court orders to free inmates to relieve overcrowding or trying alternatives to incarceration, criminologists and advocates say, the Patrick administration’s overhaul of the parole system seems likely to make prisons even more cramped.

“This will just make things worse in terms of overcrowding,’’ said Chester Britt, dean of the School of Criminology and Criminal Justice at Northeastern University. “It’s dangerous for other inmates and dangerous for the staff who works there. And the state’s not in a position where it will build new prisons.’’

But Josh Wall, the veteran Suffolk County prosecutor whom the governor has tapped as interim executive director of the agency and is Patrick’s pick for chairman of the board, said the potential impact on prisons can’t be the state’s first concern.

“The issue of overcrowding is not going to override the fundamental objective that we have right now, which is to get the parole system working and to get the confidence back in the system,’’ he said.

Wall hopes to achieve those goals, he said, by making sure the board uses an “evidence-based risk assessment’’ yardstick when deciding whether inmates can be trusted with parole, and by improving supervision of parolees.

The mass resignation Thursday of five board members who participated in a 2008 vote to parole Domenic Cinelli, a career criminal who killed a Woburn police officer Christmas weekend, will almost certainly reduce paroles to a trickle until Patrick replaces them, according to people familiar with the process.

The seven-member board has only two members left to handle the roughly 8,000 to 9,000 hearings in state prisons and county jails that are held each year.

The full board convenes at the agency’s Natick headquarters for the most serious cases, so-called lifer hearings, mostly for inmates convicted of second-degree murder, who serve sentences of 15 years to life. The panel held 88 such hearings in 2009 and paroled 35 inmates, or 40 percent, according to the most recently available statistics.

But board members also hear applications from less serious offenders, such as people convicted of assault and burglary. Parole Board members each sit in on roughly 1,300 hearings annually, individually or in panels of two or three, at prisons and jails across the state. Some 5,000 to 6,000 convicted criminals are paroled each year, serving the remainder of their sentences under supervision in the community.

The two remaining board members cannot hold lifer hearings, but they can conduct the other sessions.

Patrick has pledged to nominate successors for confirmation by the Governor’s Council as quickly as possible. But even after the board has a full complement, the new panel probably will be leery about paroling inmates who pose even a modest threat to public safety, given what happened to the board members who freed Cinelli, the lifer who killed Woburn police Officer John Maguire, said criminologists and advocates for inmates.

The five board members, including Patrick’s handpicked chairman, Mark A. Conrad, a retired Milton police officer, resigned amid fierce criticism by police chiefs and a devastating review of the agency by the Executive Office of Public Safety and Security.

The review detailed a series of missteps by the board and by agency staff in the Cinelli case. The alleged lapses included the failure of employees to inform the panel that Cinelli, while using an alias, had assaulted a Chelsea police officer in 1985 and inadequate supervision of the parolee by staff.

“Would you apply for a job if you knew that if you made one mistake, you were going to get fired?’’ Leslie Walker, executive director of Prisoners’ Legal Services, a Boston-based group that provides civil legal services to inmates, said. “So who’s going to apply? People who don’t mind saying no.’’

Britt agreed. “My sense,’’ he said, “is the Parole Board will be very reluctant to release a ‘lifer’ or anybody who’s committed a serious violent crime if there’s even the slightest indication that they could do this again.’’

Efforts to reach board members since the resignations have been unsuccessful.

Patrick has also proposed a series of changes in state law that would increase the time served by third-time criminal offenders, while tightening a variety of parole eligibility requirements. The changes are intended to address repeat offenders like Cinelli, a habitual armed robber.

Cinelli had spent about 30 years in prison and was serving three concurrent life sentences when the board voted on Nov. 18, 2008, to parole him. Nearly two years later, on Dec. 26, he shot and killed Maguire outside a Kohl’s department store following a jewelry heist. Cinelli, 57, was killed in the shoot-out.

Police chiefs, victims’ rights advocates, and lawmakers praised Patrick’s response to the Cinelli case last week. But critics say it will worsen conditions in prisons and note that nearly all inmates will eventually be freed, whether they win parole or simply complete their sentences. The prisons currently hold 11,185 inmates, 39 percent above capacity, according to Diane Wiffin, a spokeswoman for the system.

Prison overcrowding has been a major concern for years.

Last June, Harold W. Clarke, then the commissioner of the Department of Correction, publicly supported State House efforts to change mandatory minimum sentences for nonviolent drug crimes because of overcrowding. Almost 1 in 4 of the state’s criminally convicted inmates were serving mandatory minimum sentences for nonviolent crimes. Clarke has since left the job.

Cramped conditions also prompted the Patrick administration to double-bunk inmates in some cells beginning in January 2009 at Souza-Baranowski Correctional Center in Shirley. That drew sharp criticism from the Massachusetts Correction Officers Federated Union, which says the move has caused inmates to lash out at one another and at correction officers.

By the Parole Board’s own account, supervised parole of inmates suitable for release is much less expensive than imprisonment. The cost to supervise a parolee is $5,000 a year, compared with $30,000 to $40,000 to incarcerate an inmate, according to the board’s website.

Even before last week’s resignations, the Cinelli case had caused a snag in the paroling of inmates, according to Walker, of Prisoners’ Legal Services. Seven inmates who had already won parole and were to be freed soon, if they successfully completed stays in prerelease centers, were returned to prison because of the controversy, she said.

One of the men, who had been convicted of second-degree murder in 1994, was granted parole in March 2009, Walker said. He had been living at a prerelease center and working at a restaurant and was scheduled to be freed in two months.

Walker said the man’s family “can’t understand why he’s been pulled back, because he hasn’t done anything.’’

Brian Jansen, the president of the correction officers’ union, agreed that Patrick’s overhaul of the parole system will probably increase prison overcrowding, but said, “Prisons exist for a reason, and public safety should take priority over a request or a demand for parole.’’

John Grossman, Patrick’s undersecretary of public safety and one of the authors of the review of the agency, said in a statement Friday that the governor has been “consistently clear that parole is an important component of our criminal justice system.’’ Grossman did not specifically address questions of overcrowding.

Others downplayed concerns about the prisons.

Chelsea Police Chief Brian Kyes, vice president of the Massachusetts Major City Chiefs association, said overcrowding is a legitimate issue, but “I don’t think it’s a mutually exclusive equation: We’re either going to have overcrowded prisons, or we’re going to parole people who perhaps don’t deserve to be paroled.’’

Laurie Ann Myers, president of Community Voices, a Chelmsford-based nonprofit that advocates on behalf of crime victims, said she was far more concerned about violent criminals being released prematurely than prison overcrowding.

“Prisoners are adequately supervised,’’ she said in an e-mail. “I wish I could say the same about the inmates that are released into our communities.

Maria Cramer, Shelley Murphy, and Michael Rezendes of the Globe staff contributed to this report. Saltzman can be reached at jsaltzman@globe.com.